Dataset Information

Targeting pseudoknots in H5N1 hemagglutinin using designed aptamers.

ABSTRACT: Influenza A virus subtype H5N1 is highly contagious among birds, causing high mortality among domestic poultry. The viral genome is contained on eight single RNA strands of which HA encode the antigenic glycoprotein called hemagglutinin. Hemagglutinin found on the surface of the influenza viruses and is responsible for binding the virus to the cell that is being infected. Among the most prevalent RNA structures the pseudoknot motif represents an important piece of RNA architecture, as it provides a means for a single RNA strand to fold upon itself to produce a globular structure capable of performing important biological functions. In this analysis we have identified the pseudoknot motifs in the hemagglutinin gene of HPAI A (H5N1) Asian strains. Specific aptamers have been designed against these pseudoknots. These in-silico aptamers can be used to hinder the ability of pseudoknots to facilitate ribosomal frameshifting. This may ultimately lead to reduce the coding efficiency of the HA that encodes hemagglutinin and might be used as molecular medicine for H5N1.

SUBMITTER: Dhar

PROVIDER: S-EPMC2859575 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Targeting pseudoknots in H5N1 hemagglutinin using designed aptamers.

Dhar Ganguli Sayak S Datta Abhijit A

Bioinformation 20091025 5

Influenza A virus subtype H5N1 is highly contagious among birds, causing high mortality among domestic poultry. The viral genome is contained on eight single RNA strands of which HA encode the antigenic glycoprotein called hemagglutinin. Hemagglutinin found on the surface of the influenza viruses and is responsible for binding the virus to the cell that is being infected. Among the most prevalent RNA structures the pseudoknot motif represents an important piece of RNA architecture, as it provide ...[more]

PMID: 20461158

Similar Datasets

Project description:BackgroundProtection against the influenza virus by a specific antibody is relatively strain specific; meanwhile broader immunity may be conferred by cell-mediated immune response to the conserved epitopes across influenza virus subtypes. A universal broad-spectrum influenza vaccine which confronts not only seasonal influenza virus, but also avian influenza H5N1 virus is promising.MethodsThis study determined the specific and cross-reactive T cell responses against the highly pathogenic avian influenza A (H5N1) virus in four survivors and 33 non-H5N1 subjects including 10 H3N2 patients and 23 healthy individuals. Ex vivo IFN-γ ELISpot assay using overlapping peptides spanning the entire nucleoprotein (NP), matrix (M) and hemagglutinin (HA) derived from A/Thailand/1(KAN-1)/2004 (H5N1) virus was employed in adjunct with flow cytometry for determining T cell functions. Microneutralization (microNT) assay was performed to determine the status of previous H5N1 virus infection.ResultsIFN-γ ELISpot assay demonstrated that survivors nos. 1 and 2 had markedly higher T cell responses against H5N1 NP, M and HA epitopes than survivors nos. 3 and 4; and the magnitude of T cell responses against NP were higher than that of M and HA. Durability of the immunoreactivity persisted for as long as four years after disease onset. Upon stimulation by NP in IFN-γ ELISpot assay, 60% of H3N2 patients and 39% of healthy subjects exhibited a cross-reactive T cell response. The higher frequency and magnitude of responses in H3N2 patients may be due to blood collection at the convalescent phase of the patients. In H5N1 survivors, the effector peptide-specific T cells generated from bulk culture PBMCs by in vitro stimulation displayed a polyfunction by simultaneously producing IFN-γ and TNF-α, together with upregulation of CD107a in recognition of the target cells pulsed with peptide or infected with rVac-NP virus as investigated by flow cytometry.ConclusionsThis study provides an insight into the better understanding on the homosubtypic and heterosubtypic T cell-mediated immune responses in H5N1 survivors and non-H5N1 subjects. NP is an immunodominant target of cross-recognition owing to its high conservancy. Therefore, the development of vaccine targeting the conserved NP may be a novel strategy for influenza vaccine design.

Dataset Information

Targeting pseudoknots in H5N1 hemagglutinin using designed aptamers.

Publications

Targeting pseudoknots in H5N1 hemagglutinin using designed aptamers.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets